Software Demo: Multiple Alignment of Protein and DNA Sequences

If you have occasion to do multiple alignments of protein or DNA sequences, then you may be interested in trying one of several relatively new programs:

  • T-Coffee--Tree-based Consistency Objective Function for Alignment Evaluation
  • Muscle--Multiple Sequence Comparison by Log Expectation
  • ProbCons--Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

Software demonstration

Irit Orr and Shifra Ben-Dor of the WIS Bioinformatics Unit will demonstrate these tools on Monday, March 28th, at 12:00, in room 101 of the Levine Building.
The presentation will be aimed primarily at those who have previously used multiple alignment programs such as ClustalW. Please join us!

Features

T-Coffee, Muscle, and ProbCons are the newest generation of tools for creating multiple alignments of amino acid or nucleotide sequences (ProbCons works only with amino acids). These tools are available via the web and at Weizmann. The hands-on demo will discuss the advantages of each tool. Papers about Muscle and ProbCons won best paper awards at the ISMB/ECCB 2004 conference.

Features of T-Coffee:

  • Combines signals from heterogeneous sources, such as sequence-alignment programs, structure alignments, threading, manual alignment, motifs, and specific constraints
  • Improved accuracy for a modest decrease in speed
  • Combines local and global information

Features of Muscle:

  • Optimize speed, accuracy, or a compromise between the two
  • Quickly and accurately align tens or hundreds of sequences
  • Align large numbers (thousands) of sequences, though not as quickly
  • Refine existing alignments (whether obtained using Muscle or some other tool)
  • Align two profiles
  • Quickly cluster similar sequences

Features of ProbCons:

  • Uses progressive alignment scheme with consistency-based alignment techniques
  • Based on approximation to probabilistic model that can be iterated to account for multiple intermediate sequences when aligning two sequences

For more information

You can learn more at the tools' websites: T-Coffee - open in new windowMuscle - open in new windowProbCons

After the seminar, if you have questions about using these tools, please contact Irit Orr or Shifra Ben-Dor at ext. 2470 or by email at
open in new windowIrit.Orr@weizmann.ac.il or open in new windowShifra.Ben-Dor@weizmann.ac.il